How can I permanently add a schema to the LDAP server ? I am trying to implement SAMBA on a different machine and want to use ZeroShell for authentication. Ultimately, I want to get my SAMBA server to allow Windows domain logins.

The file slapd.conf is rendered from scripts.
But the scripts takes into account basic template from /root/kerbynet.cgi/template.cfg/
There you will find what you are looking for. slapd.conf which is ti be used each time you restart and recreate the /etc/slapd.conf.

Note however that this will not be persistent to a reboot as /root/ is in an image extracted at boot time.